Files in bio3d
Biological Structure Analysis

inst
inst/examples
inst/examples/hivp.pdb
inst/examples/aspirin.mol2
inst/examples/hivp_xray.fa
inst/examples/1dpx.pdb
inst/examples/hivp.dcd
inst/examples/1hel.pdb
inst/examples/test.pdb
inst/examples/transducin.fa
inst/examples/crambin.inpcrd
inst/examples/kif1a.fa
inst/examples/crambin.prmtop
inst/staticdocs
inst/staticdocs/index.r
inst/CITATION
inst/doc
inst/doc/bio3d_vignettes.html
inst/doc/bio3d_vignettes.Rmd
inst/matrices
inst/matrices/bio3d.mat
inst/matrices/pam30.mat
inst/matrices/blosum62.mat
inst/matrices/custom.mat
inst/matrices/similarity.mat
inst/matrices/emboss_properties.mat
inst/matrices/properties.mat
tests
tests/testthat.R
tests/testthat
tests/testthat/test-read.pdb.R tests/testthat/test-seqaln.R tests/testthat/test-clean.pdb.R tests/testthat/test-dssp.R tests/testthat/test-core.find.R tests/testthat/test-aa2mass.R tests/testthat/test-nma.pdbs.R tests/testthat/test-pdbsplit.R tests/testthat/test-mol2.R tests/testthat/test-cmap.R tests/testthat/test-aanma.pdbs.R tests/testthat/test-nma.R tests/testthat/test-atom2mass.R tests/testthat/test-gnm.R tests/testthat/test-read.ncdf.R tests/testthat/test-deformation.R tests/testthat/test-vector-funs.R tests/testthat/test-aanma.R tests/testthat/test-atom.select.R tests/testthat/test-pdb.annotate.R tests/testthat/test-get.pdb.R tests/testthat/test-dccm.R tests/testthat/test-pca.R tests/testthat/test-overlap.R tests/testthat/test-read.all.R tests/testthat/test-cna.R tests/testthat/test-rmsd.R tests/testthat/test-fitting.R
src
src/Makevars
src/read_pdb.cpp
src/read_crd.cpp
src/utils.h
src/utils.cpp
src/convert.h
src/gzstream.cpp
src/gzstream.h
src/read_cif.cpp
src/init.c
src/RcppExports.cpp
src/read_prmtop.cpp
NAMESPACE
demo
demo/pca.R
demo/00Index
demo/md.R demo/pdb.R demo/nma.R
NEWS
data
data/kinesin.RData
data/elements.rda
data/transducin.RData
data/atom.index.rda
data/sdENM.RData
data/hivp.RData
data/aa.index.rda
data/aa.table.rda
R
R/pca.tor.R R/is.select.R R/rmsd.R R/print.fasta.R R/dssp.pdb.R R/angle.xyz.R R/pdbaln.R R/entropy.R R/normalize.vector.R R/hclustplot.R R/dm.xyz.R R/as.select.R R/pca.array.R R/pdb2aln.R R/gnm.R R/print.prmtop.R R/mktrj.nma.R R/write.ncdf.R R/is.gap.R R/cnapath.R R/plot.pca.score.R R/dssp.xyz.R R/pca.R R/summary.cnapath.R R/sse.bridges.R R/print.core.R R/atom2xyz.R R/filter.identity.R R/mktrj.R R/mono.colors.R R/vmd.cnapath.R R/atom.select.mol2.R R/as.xyz.R R/plot.nma.R R/community.aln.R R/as.pdb.R R/pairwise.R R/read.all.R R/read.pqr.R R/pdbs2pdb.R R/mktrj.pca.R R/nma.pdb.R R/print.geostas.R R/prune.cna.R R/write.pir.R R/binding.site.R R/read.crd.amber.R R/get.blast.R R/read.fasta.pdb.R R/gnm.pdbs.R R/write.fasta.R R/plot.geostas.R R/print.cna.R R/plotb3.R R/mktrj.enma.R R/dccm.xyz.R R/stride.R R/dccm.enma.R R/trim.pdbs.R R/read.pdcBD.R R/rgyr.R R/dccm.gnm.R R/write.pdb.R R/rtb.R R/dccm.R R/atom.select.R R/cna.ensmb.R R/mustang.R R/is.mol2.R R/get.pdb.R R/deformation.nma.R R/read.crd.R R/pfam.R R/motif.find.R R/read.pdb2.R R/read.prmtop.R R/project.pca.R R/gap.inspect.R R/pymol.modes.R R/load.enmff.R R/print.sse.R R/conserv.R R/xyz2atom.R R/pdbfit.R R/torsion.xyz.R R/plot.fasta.R R/basename.pdb.R R/read.dcd.R R/read.fasta.R R/aln2html.R R/lbio3d.R R/filter.rmsd.R R/plot.cna.R R/pca.pdbs.R R/dist.xyz.R R/summary.cna.R R/read.pdb.R R/pdbsplit.R R/vmd_colors.R R/com.pdb.R R/pdb2aln.ind.R R/formula2mass.R R/seqbind.R R/var.xyz.R R/write.mol2.R R/cov.nma.R R/unbound.R R/vmd.R R/covsoverlap.R R/atom2mass.R R/plot.pca.loadings.R R/dccm.nma.R R/uniprot.R R/com.R R/summary.pdb.R R/mask.dccm.R R/filter.dccm.R R/atom2ele.R R/plot.hmmer.R R/inner.prod.R R/biounit.R R/rle2.R R/trim.xyz.R R/bwr.colors.R R/read.crd.charmm.R R/get.seq.R R/aanma.pdbs.R R/plot.pca.scree.R R/diag.ind.R R/is.xyz.R R/pdb2sse.R R/network.amendment.R R/read.cif.R R/aanma.R R/plot.dmat.R R/seqaln.pair.R R/pdbs2sse.R R/clean.pdb.R R/print.select.R R/plot.enma.R R/orient.pdb.R R/bounds.R R/plot.dccm.R R/RcppExports.R R/store.atom.R R/blast.pdb.R R/geostas.R R/pdb.pfam.R R/seqidentity.R R/cna.R R/sip.R R/print.pca.R R/dssp.pdbs.R R/rmsf.R R/plot.core.R R/aa123.R R/plot.pca.R R/aa2mass.R R/aa321.R R/read.mol2.R R/dssp.R R/plot.matrix.loadings.R R/layout.cna.R R/inspect.connectivity.R R/overlap.R R/trim.mol2.R R/rot.lsq.R R/amsm.xyz.R R/lmi.R R/vec2resno.R R/identify.cna.R R/vmd.cna.R R/bounds.sse.R R/aanma.pdb.R R/pymol.pdbs.R R/atom.select.pdb.R R/setup.ncore.R R/fit.xyz.R R/build.hessian.R R/nma.pdbs.R R/check.utility.R R/nma_funs.R R/cov2dccm.R R/read.ncdf.R R/difference.vector.R R/write.crd.R R/community.tree.R R/dm.R R/torsion.pdb.R R/cmap.R R/is.pdb.R R/dccm.pca.R R/cat.pdb.R R/as.pdb.mol2.R R/fluct.nma.R R/cmap.pdb.R R/plot.rmsip.R R/seq2aln.R R/core.find.R R/pymol.dccm.R R/com.xyz.R R/aa2index.R R/plot.fluct.R R/chain.pdb.R R/bhattacharyya.R R/pdb.annotate.R R/hmmer.R R/cna.dccm.R R/as.pdb.prmtop.R R/rmsip.R R/combine.select.R R/wrap.tor.R R/trim.pdb.R R/write.pqr.R R/seqaln.R R/print.xyz.R R/struct.aln.R R/atom.select.prmtop.R R/plot.cmap.R R/print.pdb.R R/pdbseq.R R/print.enma.R R/as.fasta.R R/nma.R R/filter.cmap.R R/plot.blast.R R/convert.pdb.R R/consensus.R R/print.nma.R R/pca.xyz.R
vignettes
vignettes/bio3d_vignettes.Rmd README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/seqbind.Rd man/cov.nma.Rd man/aln2html.Rd man/biounit.Rd man/read.ncdf.Rd man/orient.pdb.Rd man/pdbsplit.Rd man/plot.dccm.Rd man/core.find.Rd man/bhattacharyya.Rd man/atom2mass.Rd man/seqidentity.Rd man/plot.pca.loadings.Rd man/unbound.Rd man/bounds.sse.Rd man/entropy.Rd man/community.tree.Rd man/filter.rmsd.Rd man/atom.index.Rd man/clean.pdb.Rd man/motif.find.Rd man/pdb.annotate.Rd man/torsion.xyz.Rd man/write.pqr.Rd man/aa2mass.Rd man/conserv.Rd man/pfam.Rd man/read.pdcBD.Rd man/is.select.Rd man/dccm.nma.Rd man/vmd.cna.Rd man/is.xyz.Rd man/geostas.Rd man/dccm.gnm.Rd man/write.crd.Rd man/rgyr.Rd man/atom2xyz.Rd man/read.pqr.Rd man/aanma.pdb.Rd man/get.seq.Rd man/read.crd.charmm.Rd man/dccm.xyz.Rd man/sip.Rd man/read.fasta.Rd man/example.data.Rd man/trim.pdbs.Rd man/vmd_colors.Rd man/covsoverlap.Rd man/overlap.Rd man/sdENM.Rd man/com.Rd man/pdbs2pdb.Rd man/setup.ncore.Rd man/plot.nma.Rd man/seqaln.Rd man/cnapath.Rd man/gnm.Rd man/bounds.Rd man/print.core.Rd man/hmmer.Rd man/pdbaln.Rd man/write.pdb.Rd man/inspect.connectivity.Rd man/mktrj.Rd man/trim.xyz.Rd man/angle.xyz.Rd man/write.mol2.Rd man/plot.cna.Rd man/pdb2aln.Rd man/trim.mol2.Rd man/bwr.colors.Rd man/read.pdb.Rd man/print.fasta.Rd man/get.pdb.Rd man/layout.cna.Rd man/pdbs2sse.Rd man/mustang.Rd man/as.select.Rd man/inner.prod.Rd man/pdbfit.Rd man/read.fasta.pdb.Rd man/print.xyz.Rd man/plot.cmap.Rd man/atom.select.Rd man/seq2aln.Rd man/binding.site.Rd man/seqaln.pair.Rd man/store.atom.Rd man/pca.tor.Rd man/var.xyz.Rd man/atom2ele.Rd man/plot.dmat.Rd man/combine.select.Rd man/read.crd.Rd man/prune.cna.Rd man/basename.pdb.Rd man/dccm.Rd man/plot.fasta.Rd man/deformation.nma.Rd man/check.utility.Rd man/aa.table.Rd man/write.fasta.Rd man/lmi.Rd man/fit.xyz.Rd man/read.cif.Rd man/plot.hmmer.Rd man/torsion.pdb.Rd man/pairwise.Rd man/pca.xyz.Rd man/consensus.Rd man/pymol.Rd man/rle2.Rd man/write.pir.Rd man/mask.dccm.Rd man/fluct.nma.Rd man/normalize.vector.Rd man/is.gap.Rd man/pca.array.Rd man/as.fasta.Rd man/pca.pdbs.Rd man/diag.ind.Rd man/aa123.Rd man/filter.identity.Rd man/vec2resno.Rd man/hclustplot.Rd man/read.crd.amber.Rd man/as.pdb.Rd man/elements.Rd man/is.pdb.Rd man/blast.pdb.Rd man/dssp.Rd man/pdbseq.Rd man/nma.Rd man/load.enmff.Rd man/dccm.pca.Rd man/pca.Rd man/identify.cna.Rd man/nma.pdbs.Rd man/difference.vector.Rd man/pdb2sse.Rd man/dccm.enma.Rd man/formula2mass.Rd man/plot.enma.Rd man/network.amendment.Rd man/chain.pdb.Rd man/bio3d.package.Rd man/read.dcd.Rd man/rmsip.Rd man/aa2index.Rd man/struct.aln.Rd man/cna.Rd man/dm.Rd man/aa.index.Rd man/write.ncdf.Rd man/dist.xyz.Rd man/filter.cmap.Rd man/wrap.tor.Rd man/lbio3d.Rd man/sse.bridges.Rd man/cmap.Rd man/community.aln.Rd man/rmsf.Rd man/is.mol2.Rd man/plot.rmsip.Rd man/filter.dccm.Rd man/plot.matrix.loadings.Rd man/nma.pdb.Rd man/read.mol2.Rd man/aanma.pdbs.Rd man/project.pca.Rd man/cat.pdb.Rd man/gap.inspect.Rd man/convert.pdb.Rd man/uniprot.Rd man/plot.bio3d.Rd man/plot.pca.Rd man/plot.fluct.Rd man/print.cna.Rd man/rmsd.Rd man/plot.core.Rd man/pdb2aln.ind.Rd man/trim.pdb.Rd man/plot.geostas.Rd man/read.prmtop.Rd man/read.all.Rd
bio3d documentation built on July 31, 2017, 9:01 a.m.